On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data.

We consider the problem of inferring fold changes in gene expression from cDNA microarray data. Standard procedures focus on the ratio of measured fluorescent intensities at each spot on the microarray, but to do so is to ignore the fact that the variation of such ratios is not constant. Estimates of gene expression changes are derived within a simple hierarchical model that accounts for measurement error and fluctuations in absolute gene expression levels. Significant gene expression changes are identified by deriving the posterior odds of change within a similar model. The methods are tested via simulation and are applied to a panel of Escherichia coli microarrays.     

Cross-sectional geometric analysis of a foot bone assemblage from Mangaia, Cook Islands

This study describes a human foot bone assemblage from prehistoric Mangaia, Cook Islands in the context of diaphyseal cross-sectional strength measures. We use this sample to test the hypothesis that habitually unshod individuals who walk over rugged terrain will have stronger foot bones than a sample of habitually shod industrialized people. Specifically, we examine whether the Mangaian sample has a stronger size-adjusted metatarsal (MT) and phalangeal cross-sectional properties than the industrial sample, drawn from the Terry Collection. Contrary to expectations, residual analyses showed that most values of cross-sectional area (CA) and torsional resistance (J) of MTs 1-4 and the hallucal proximal phalanx (HPP) of the Mangaians are among those in the lower range of the Terry Collection sample. However, the bending strength ratios (Zy/Zx) of the Mangaian HPP are significantly greater than those of the Terry Collection. While characteristics such as forefoot shape variation between the sexes and among geographic populations cannot be ruled out as influential factors, cross-sectional properties of the hallucal proximal phalanges, but not the MTs, indicate terrain complexity in prehistoric populations.     

X-ray diffraction study of a new crystal form of the nucleosome core showing higher resolution

Crystals have been grown of intact (unproteolysed) nucleosome cores from a variety of sources. The unit cells are all very similar, with one core particle per asymmetric unit. The X-ray diffraction patterns extend to about 5 Å in the direction perpendicular to the plane of the flat particle, and to somewhat less than this in other directions. The arrangement of particles in the unit cell has been deduced from Patterson projection maps, which also indicate the presence of a particle dyad. The data are consistent with the earlier proposed model for the core particle in which the 146 base-pairs of DNA are wound in about $\text{1}\text{3}\text{4}$ turns of superhelix about a histone octamer core.High angle diffuse X-ray scattering from the crystals shows that the DNA of the core particle is in the B form. The anisotropy of the diffuse scattering shows that the DNA is not firmly fixed to the histone core all along the superhelix path, but only over limited regions whose location correlates well with those in which the DNA is differentially protected against nuclease digestion.     

The localization of the nuclear protein pool in Xenopus oocytes

It has been demonstrated previously that nuclear proteins in Xenopus oocytes are synthesized in the cytoplasm and maintained in a cellular pool. The present study was performed to determine if any portion of this pool is associated specifically with the nuclear envelope. This was accomplished by first micro-injecting oocytes with [³H]leucine; at various times after injection, nuclear envelope and nucleoplasmic fractions were run on SDS-polyacrylamide gels. In this way labeled polypeptides available in the envelope fraction could be compared to polypeptides which were subsequently incorporated into the nucleoplasm. No evidence was obtained that the nuclear protein pool is associated with the envelope.